Tim's repositories
neurocontainers
The containers can be used in combination with our transparent singularity or neurocommand tool, that wrap the executables inside a container to make them easily available for pipelines
afni
Official AFNI source and documentation
apptainer
Apptainer: Application containers for Linux
bart
BART: Toolbox for Computational Magnetic Resonance Imaging
bartpy
Python wrappers for external BART computational imaging tools and internal libraries
brkraw
BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data
brkraw-snippets
BrkRaw Snippets: Modular Extensions for BrkRaw
chi-separation
Code for magnetic susceptibility source separation
CoSimPy
Python electromagnetic cosimulation library
Docker-OSX
Run macOS VM in a Docker! Run near native OSX-KVM in Docker! X11 Forwarding! CI/CD for OS X Security Research! Docker mac Containers.
finufft
Non-uniform fast Fourier transform library of types 1,2,3 in dimensions 1,2,3
gadgetron
Gadgetron - Medical Image Reconstruction Framework
gpuNUFFT
gpuNUFFT - An Open-Source GPU Library for 3D Gridding with Direct Matlab and Python Interface
hackbat
Hackbat repository
ismrmrd
ISMRM Raw Data Format
KomaMRI.jl
Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.
LTSpice_on_Linux_Ubuntu__How_to_install_and_use
Make great analog designs
mirt
Michigan Image Reconstruction Toolbox (MIRT) - Matlab version
MIRT.jl
MIRT: Michigan Image Reconstruction Toolbox (Julia version)
monte-carlo-simulation-recipes
Recipes of Monte Carlo simulations in Fieremans and Lee, NeuroImage 2018
mri-nufft
Doing non-Cartesian MR Imaging has never been so easy.
MRIReco.jl
Julia Package for MRI Reconstruction
MriResearchTools.jl
Specialized tools for MRI
openpilot
openpilot is an open source driver assistance system. openpilot performs the functions of Automated Lane Centering and Adaptive Cruise Control for 250+ supported car makes and models.
pulseq
Open source framework for pulse sequences
python-ismrmrd-server
Example client/server example for the streaming ISMRM Raw Data protocol
reproduce-l-s-dynamic-mri
Matlab code for reproducing 2019 IEEE Tr. Comp. Im. paper "Efficient Dynamic Parallel MRI Reconstruction for the Low-Rank Plus Sparse Model" by Claire Lin
sepia
Matlab GUI pipeline application for quantitative susceptibility mapping (QSM)
timwahoo
Config files for my GitHub profile.
twixtools
python file reader/writer for Siemens MRI raw data + compression utility